The Set Matte effect is actually a legacy effect from before Adobe owned AE. (that was the only way to do “track matte”s back then) But it’s still so useful for things, like you pointed out – to be able to matte things procedurally so users of the file don’t have to dig and you don’t have to worry about layer hierarchy.
The really great thing is that you can keep a layer’s original alpha (by selecting “comp matte with original” in the effect) and now you have technically two alpha’s at work: the layer you point to with the Set matte effect, and the layer’s own alpha from a rendered source or PShop (or if the layer is precomp with alpha info). You can then go one better by putting that layer with the setMatte effect below another and using track matte to triple matte the layer.
This of course could all be done by precomping the original and then just trackmatting the outer layer again, but often you want to preserve a blend/transfer mode (which can be lost with a precomp) or you have mixed 2D and 3D stuff going on and precomping suddenly sends your layer into the Forbidden Zone as the 3D camera tries to reposition it in a new WorldSpace. And yes, you can do some fancy “toWorld, fromWorld” stuff to reign that back in, but why bother?